Consortium Research Platform on Genomics

ICAR-National Bureau of Agricultural Important Micro-organism (NBAIM), Mau

Microorganisms are the most abundant organisms on Earth with a total diversity of prokaryotes comprising up to 109 species and an estimated number of 2.27 million fungi. For prokaryotic species, only new names published in the International Journal of Systematic and Evolutionary Microbiology (IJSEM) as an original article or in the "Validation Lists" are considered valid. As of the end of 2017, 15448 valid prokaryotic species were published. The IJSEM announced, from January 2018, authors of new taxa descriptions have been asked to provide genome sequence data with descriptions of novel taxa with their manuscript submissions. Hence the taxonomy of prokaryotes has entered into genomic era making it mandatory to sequence whole genome to describe a species. Microorganisms possess extensive genomic and metabolic diversity, which makes them ideal biotechnological tools. Decoding the full genomes of various species in order to provide reference genomes will thus enable genes to be associated with functions, such as metabolic activity, virulence, antibiotic production or resistance, biomass deconstruction, agricultural nitrogen fixation, and the liberation of environmental phosphorus.

The number of sequenced genomes has continued to increase dramatically in the last 10 years, there are more than 34866 sequenced bacterial genomes currently publically available in (NCBI 2019) and thousands of metagenome projects (GOLD 2019). Projects such as the Genomic Encyclopedia of Bacteria and Archaea (GEBA) (Kyrpides et al. 2014) promise to not only add more genomes but expand the genetic diversity and add to the list of available types of strains. The nature of data to be analyzed is changing with adavancement in technologies. For example, microarray analysis of transcriptomes is being replaced by RNA sequencing, which has some substantial advantages, although the statistical analysis packages for this data are continually evolving and are by no means standardized. The stories revealed from analysis of these sample metagenomes, especially the human microbiomes, have dramatically changed our view of the microbial world to the point that the general public is now aware of the possible beneficial effects of bacteria on their health and not just as the source of illness.

Access to microbial genomic sequences will significantly contribute to future studies in microbial biology, ecology, and biochemistry and these will, in turn, accelerate the discovery of new natural products and drugs. Presently, the selection of strains for whole-genome sequencing is based predominantly on medical, ecological, or industrial importance, which often leads to bias against agriculturally important microorganisms.

Objective

1. To sequence approximately 130 niche and trait specific microorganism including archea. The strains have emerged as potential AIMs from the microbial diversity and community analysis of extreme region by the Bureau
2. Mining of genes/alleles of different industrially and agriculturally important traits.
3. Genome sequences will further be used for comparative studies with the bacteria isolated from other regions using genome sequences generated.

Research targets/activities

1. Genome sequencing of abiotic stress ameliorating bacteria/archea from extreme habitats
2. Genome sequencing of antifreeze producing bacteria and elite microbial strains involved in plant health and stress management
3. Transcriptome sequencing and functional validation of selected microbial strains. ANJ207.